Search NASA⌕ Search

SEARCH · Search NASA

Results for “fragmentation functions”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

The role of irradiation-enhanced interstitial diffusion in over-pressurizing fission gas bubbles in UO 2

Fission gas bubbles in UO 2 nuclear fuel have been observed to exhibit pressures in excess of the equilibrium bubble pressure; however, the cause of bubble over-pressurization has not yet been demonstrated. The mechanical interaction between a bubble and the surrounding matrix or grain boundary depends on the internal pressure of the bubble and local stress state, such that over-pressurized bubbles are thought to be responsible for fragmentation and pulverization, when exposed to a temperature ramp. Here, in this work, we investigate the role of U interstitials, produced through irradiation, in over-pressurizing bubbles by using a combined molecular dynamics (MD) and cluster dynamics approach. Firstly, the energies for the capture of interstitials and vacancies by bubbles have been determined from MD as a function of the ratio of gas atoms to vacancies that make up the bubble. Secondly, these reaction energies have been implemented in the cluster dynamics code Centipede to predict bubble over-pressurization as a function of temperature for typical fission rates. It was found that there is a transition from low pressure bubbles (at high temperatures) to high pressure bubbles (at lower temperatures). The cause of this behavior was shown to be the creation of irradiation-induced interstitials that are highly mobile relative to vacancies at low temperature; whereas, vacancies are sufficiently mobile at high temperatures to limit bubble pressures. This result supports the hypothesis that over-pressurized bubbles form during steady-state operation and that this behavior is highly sensitive to the local pellet temperature.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Probing C–I bond fission in the UV photochemistry of 2-iodothiophene with core-to-valence transient absorption spectroscopy

The UV photochemistry of small heteroaromatic molecules serves as a testbed for understanding fundamental photo-induced chemical transformations in moderately complex compounds, including isomerization, ring-opening, and molecular dissociation. Here, a combined experimental-theoretical study of 268 nm UV light-induced dynamics in 2-iodothiophene (C 4 H 3 IS) is performed. The dynamics are experimentally monitored with a femtosecond extreme ultraviolet (XUV) probe that measures iodine N-edge 4d core-to-valence transitions. Experiments are complemented by density functional theory calculations of both the pump-pulse induced valence excitations and the XUV probe-induced core-to-valence transitions. Possible intramolecular relaxation dynamics are investigated by ab initio molecular dynamics simulations. Furthermore, gradual absorption changes up to ~0.5 to 1 ps after excitation are observed for both the parent molecular species and emerging iodine fragments, with the latter appearing with a characteristic rise time of 160 ± 30 fs. Comparison of spectral intensities and energies with the calculations identifies an iodine dissociation pathway initiated by a predominant π → π* excitation. In contrast, initial excitation to a nearby n ⟂ → σ* state appears unlikely based on a significantly smaller oscillator strength and the absence of any corresponding XUV absorption signatures. Excitation to the π → π* state is followed by contraction of the C–I bond, enabling a nonadiabatic transition to a dissociative π→σ C-I * state. For the subsequent fragmentation, a relatively narrow bond-length region along the C–I stretch coordinate between 230 and 280 pm is identified, where the transition between the parent molecule and the thienyl radical + iodine atom products becomes prominent in the XUV spectrum due to rapid localization of two singly occupied molecular orbitals on the two fragments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Supported Organoiridium-Pincer Catalysts for the Nonoxidative Dehydrogenation of High-Density Polyethylene

The iridium-pincer complex {p-OP( t Bu) 2 -C 6 H 2 -2,6-OP( t Bu) 2 ] 2 }Ir(C 2 H 4 ) ( P [Ir]) has been reported as a stable and active catalyst toward alkane dehydrogenation in homogeneous and supported heterogeneous systems. Dehydrogenation has been shown as a practical method toward functional polyolefins, with dehydrogenated high-density polyethylene (deHDPE) demonstrated as a valuable synthon for upcycling, as orthogonal C-H strategies are key to end-of-life upcycling. The heterogenization of P [Ir] on oxides (SiO 2 , Al 2 O 3 , and TiO 2 ; P [Ir]/E y O x ) yields a mixture of organometallic Ir-fragments whose catalytic nonoxidative dehydrogenation activity is modulated by the binding modes of the active metal on the surface. The binding mode was elucidated by a combination of solid-state NMR and XAFS analyses and supported by DFT calculations. Surface binding through the ligand enables active organoiridium that catalyzes internal olefination of deHDPE up to 1.23 mol % at 200 °C under dynamic vacuum. Alternatively, when the organoiridium is bonded though the metal center (Ir-O SiO ), catalyst activity is negligible. Furthermore, the catalytic activity of P [Ir]/SiO 2 showed comparable reactivity with the homogeneous analogue under the same catalytic conditions, and the heterogenized catalyst can be reused up to three cycles. In conclusion, this work highlights the importance of understanding how organometallic precursors react with hydroxylated metal oxide surfaces to establish structure-property relationships.

Hunt, Samuel B. [Argonne National Laboratory (ANL)↗
DOE OSTI2021

Topochemical Deintercalation of Li from Layered LiNiB: toward 2D MBene

The pursuit of two-dimensional (2D) borides, MBenes, has proven to be challenging, not the least because of the lack of a suitable precursor prone to the deintercalation. Here, we studied room-temperature topochemical deintercalation of lithium from the layered polymorphs of the LiNiB compound with a considerable amount of Li stored in between [NiB] layers (33 at. % Li). Deintercalation of Li leads to novel metastable borides (Li~ 0.5 NiB) with unique crystal structures. Partial removal of Li is accomplished by exposing the parent phases to air, water, or dilute HCl under ambient conditions. Scanning transmission electron microscopy and solid-state 7 Li and 11 B NMR spectroscopy, combined with X-ray pair distribution function (PDF) analysis and DFT calculations, were utilized to elucidate the novel structures of Li~ 0.5 NiB and the mechanism of Li-deintercalation. We have shown that the deintercalation of Li proceeds via a “zip-lock” mechanism, leading to the condensation of single [NiB] layers into double or triple layers bound via covalent bonds, resulting in structural fragments with Li[NiB] 2 and Li[NiB] 3 compositions. The crystal structure of Li~ 0.5 NiB is best described as an intergrowth of the ordered single [NiB], double [NiB] 2 , or triple [NiB] 3 layers alternating with single Li layers; this explains its structural complexity. Here, the formation of double or triple [NiB] layers induces a change in the magnetic behavior from temperatureindependent paramagnets in the parent LiNiB compounds to the spin-glassiness in the deintercalated Li~ 0.5 NiB counterparts. LiNiB compounds showcase the potential to access a plethora of unique materials, including 2D MBenes (NiB).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Cytochrome P450 BM3 enzyme variants for preparation of cyclopropanes

The present invention provides methods for catalyzing the conversion of an olefin to any compound containing one or more cyclopropane functional groups using heme enzymes. In certain aspects, the present invention provides a method for producing a cyclopropanation product comprising providing an olefinic substrate, a diazo reagent, and a heme enzyme; and admixing the components in a reaction for a time sufficient to produce a cyclopropanation product. In other aspects, the present invention provides heme enzymes including variants and fragments thereof that are capable of carrying out in vivo and in vitro olefin cyclopropanation reactions. Expression vectors and host cells expressing the heme enzymes are also provided by the present invention.

Coelho, Pedro S.↗
DOE OSTI2020

Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition

Abstract Adenosine deaminases acting on RNA (ADARs) are enzymes that convert adenosine to inosine in duplex RNA, a modification that exhibits a multitude of effects on RNA structure and function. Recent studies have identified ADAR1 as a potential cancer therapeutic target. ADARs are also important in the development of directed RNA editing therapeutics. A comprehensive understanding of the molecular mechanism of the ADAR reaction will advance efforts to develop ADAR inhibitors and new tools for directed RNA editing. Here we report the X-ray crystal structure of a fragment of human ADAR2 comprising its deaminase domain and double stranded RNA binding domain 2 (dsRBD2) bound to an RNA duplex as an asymmetric homodimer. We identified a highly conserved ADAR dimerization interface and validated the importance of these sequence elements on dimer formation via gel mobility shift assays and size exclusion chromatography. We also show that mutation in the dimerization interface inhibits editing in an RNA substrate-dependent manner for both ADAR1 and ADAR2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling the Impact of the Organic Aerosol Phase State on Multiphase OH Reactive Uptake Kinetics and the Resultant Heterogeneous Oxidation Timescale of Organic Aerosol in the Amazon Rainforest

Accurate predictions of chemical lifetime, i.e., oxidation timescale and change in the mass of organic aerosols (OAs) in atmospheric models, are critical to quantify the impacts of OA on aerosol–cloud interactions, radiative forcing, and air quality. The heterogeneous oxidation of OA by hydroxyl (OH) radicals is a key process governing OA mass changes during their oxidation. Recently, laboratory observations of the OH uptake coefficient (γ OH ) and heterogeneous reaction rate (k het,OH ) for different OA systems with varying phase states have been combined to develop a new parameterization of γ OH and k het,OH as a function of the OA phase state, i.e., viscosity (η OA ). Here, in this work, we use a recently published viscosity prediction framework to analyze the new γ OH and k het,OH parameterization with a box model. Subsequently, we implement this box model to predict γ OH and k het,OH over the Amazon rainforest in the dry-to-wet transition season with both significant biomass burning and biogenic influences. Relevant parameters within our box model are specified based on detailed regional model simulations over the Amazon using the Weather Research and Forecasting model coupled with Chemistry (WRF-Chem). η OA is predicted as a function of species volatility, OA composition (including water uptake) along with ambient relative humidity (RH), and temperature. Based on ambient conditions simulated by WRF-Chem over the entire atmospheric column, we use the box model to predict the upper bounds of the heterogeneous oxidation timescale of OA. Based on previous laboratory measurements, we assume that this heterogeneous OH oxidation causes fragmentation (carbon loss) of OA, followed by the evaporation of the fragmented molecules that results in the exponential decay of OA. We predict that the oxidation timescale of OA is ~1 month near the Earth’s surface in the pristine Amazonian background because of low OH concentrations. But OA is oxidized more rapidly within urban and wildfire plumes near the Earth’s surface with an order of magnitude higher OH concentrations compared to the pristine background, causing the simulated oxidation timescale of OA to be much shorter, ~3–4 days. At 3–5 km altitudes where biomass burning OA is predicted to be semisolid, the heterogeneous oxidation timescale is estimated as ~6 days to 3 weeks and decreases with increasing OH concentrations within plumes. We show that the simulated mass loss of OA is strongly size-dependent, where smaller particles oxidize more rapidly compared to larger particles due to their greater per-particle surface area-to-volume ratio. Increasing urbanization and deforestation in the Amazon in the future might increase OH concentrations in the background Amazon, causing faster oxidation of OA. At higher altitudes above liquid clouds, especially in the upper troposphere where temperatures approach ~250 K, future measurements are needed to reduce the uncertainties related to the mass loss of OA at colder temperatures and low relative humidity conditions due to its heterogeneous OH oxidation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Kinetic Study of Polyvinyl Chloride Pyrolysis with Characterization of Dehydrochlorinated PVC

In this paper, we study the kinetics of polyvinyl chloride (PVC) decomposition using a combination of experimental and computational approaches. Here, we develop a simplified kinetic model that contains only two steps: dehydrochlorination of PVC and further decomposition of the PVC residue. The model is consistent with density functional theory (DFT) calculations and experimental data. Dehydrochlorination is an autocatalytic reaction that starts with a tertiary chloride (Cl) and generates hydrogen chloride (HCl) and benzene as the main products. Benzene and HCl formation rates showed similar trends, indicating that HCl likely catalyzes a homolytic carbon-carbon (C-C) bond cleavage, which gives rise to benzene and an aliphatic fragment. We characterized the structure of dehydrochlorinated PVC (PVC residue) by using thermal gravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FTIR), and nuclear magnetic resonance spectroscopy (NMR). FTIR and NMR results indicate that the PVC residue contains 20% quaternary carbon content, indicating a high concentration of cross-linked molecules. We predict that the most probable structure in the cross-linked centers of the PVC residue is cyclohexadiene, which is supported by DFT calculations, FTIR, and NMR.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Four α correlations in nuclear fragmentation: a game of resonances *

Abstract Heavy ion collisions near the Fermi energy produce a ‘freezout’ region where fragments appear and later decay, emitting mainly neutrons, protons, alpha particles, and gamma rays. These decay products carry information about the decaying nuclei. Fragmentation events may result in high yields of boson particles, especially alpha particles, and may carry important information about the nuclear Bose Einstein condensate (BEC). We study ‘in medium’ four α correlations and link them to the ‘fission’ of 16 O in two 8 Be in the ground state or 12 C * (Hoyle state)+ α . Using novel techniques for the correlation functions, we confirm the resonance of 16 O at 15.2 MeV excitation energy, and the possibility of a lower resonance, close to 14.72 MeV. The latter resonance is the result of all α particles having 92 keV relative kinetic energies.

Physics↗
DOE OSTI2020

A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large–scale systems–level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high–throughput enhanced yeast one–hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis–regulatory elements (CREs) in ER stress–responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Lastly, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription–regulatory mechanisms in the stress responses and crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure --- this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗
DOE OSTI2022

SPATIAL GRAPH ATTENTION AND CURIOSITY-DRIVEN POLICY FOR ANTIVIRAL DRUG DISCOVERY

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure - this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Y↗
DOE OSTI2021

Evaluating the effects of structural disorder on the magnetic properties of Nd 2 Zr 2 O 7

Motivated by the variation in reported lattice parameters of floating-zone-grown Nd 2 Zr 2 O 7 crystals, we have performed a detailed study of the relationship between synthesis environment, structural disorder, and magnetic properties. Using a combination of polycrystalline standards, electron-probe microanalysis, and scattering techniques, we show that crystals grown under atmospheric conditions have a reduced lattice parameter relative to pristine polycrystalline powders due to occupation of the Nd site by excess Zr (i.e., negative stuffing). In contrast, crystals grown under high-pressure Ar are nearly stoichiometric with an average lattice parameter approaching the polycrystalline value. While minimal disorder of the oxygen sublattices is observed on the scale of the average structure, neutron pair-distribution function analysis indicates a highly local disorder of the oxygen coordination, which is only weakly dependent on growth environment. Most importantly, our magnetization, heat capacity, and single-crystal neutron scattering data show that the magnetic properties of crystals grown under high-pressure Ar match closely with those of stoichiometric powders. Neutron scattering measurements reveal that the signature of magnetic moment fragmentation—the coexistence of all-in-all-out (AIAO) magnetic Bragg peaks and diffuse pinch-point scattering due to spin-ice correlations–persists in these nearly stoichiometric crystals. However, in addition to an increased AIAO transition temperature, the diffuse signal is seemingly stabilized and remains nearly unchanged upon warming to 800 mK. This behavior indicates that both the AIAO magnetic order and spin-ice correlations are sensitive to deviations of the Nd stoichiometry.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Neutralizing epitopes on Clostridioides difficile toxin A revealed by the structures of two camelid VHH antibodies

Toxin A (TcdA) and toxin B (TcdB) are two key virulence factors secreted by Clostridioides difficile, which is listed as an urgent threat by the CDC. These two large homologous exotoxins are mainly responsible for diseases associated with C. difficile infection (CDI) with symptoms ranging from diarrhea to life threatening pseudomembranous colitis. Single-domain camelid antibodies (VHHs) AH3 and AA6 are two potent antitoxins against TcdA, which when combined with two TcdB-targeting VHHs showed effective protection against both primary and recurrent CDI in animal models. Here, we report the co-crystal structures of AH3 and AA6 when they form complexes with the glucosyltransferase domain (GTD) and a fragment of the delivery and receptor-binding domain (DRBD) of TcdA, respectively. Based on these structures, we find that AH3 binding enhances the overall stability of the GTD and interferes with its unfolding at acidic pH, and AA6 may inhibit the pH-dependent conformational changes in the DRBD that is necessary for pore formation of TcdA. These studies reveal two functionally critical epitopes on TcdA and shed new insights into neutralizing mechanisms and potential development of epitope-focused vaccines against TcdA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Charge radii in covariant density functional theory: A global view

A systematic global investigation of differential charge radii has been performed within the CDFT framework for the first time. Theoretical results obtained with conventional covariant energy density functionals and the separable pairing interaction of Tian et al. [Phys. Lett. B 676, 44 (2009)] are compared with experimental differential charge radii in the regions of the nuclear chart in which available experimental data crosses the neutron shell closures at N=28,50,82, and 126. The analysis of absolute differential radii of different isotopic chains and their relative properties indicate clearly that such properties are reasonably well described in model calculations in the cases when the mean-field approximation is justified. However, while the observed clusterization of differential charge radii of different isotopic chains is well described above the N=50 and N=126 shell closures, it is more difficult to reproduce it above the N=28 and N=82 shell closures because of possible deficiencies in the underlying single-particle structure. The impact of the latter has been evaluated for spherical shapes and it was shown that the relative energies of the single-particle states and the patterns of their occupation with increasing neutron number have an appreciable impact on the evolution of the δ$\langle$r2$\rangle$N,N' values. These factors also limit the predictive power of model calculations in the regions of high densities of the single-particle states of different origin. It is shown that the kinks in the charge radii at neutron shell closures are due to the underlying single-particle structure and due to weakening or collapse of pairing at these closures. The regions of the nuclear chart in which the correlations beyond mean field are expected to have an impact on charge radii are indicated; the analysis shows that the assignment of a calculated excited prolate minimum to the experimental ground state allows us to understand the trends of the evolution of differential charge radii with neutron number in many cases of shape coexistence even at the mean-field level. It is usually assumed that pairing is a dominant contributor to odd-even staggering (OES) in charge radii. Our analysis paints a more complicated picture. It suggests a new mechanism in which the fragmentation of the single-particle content of the ground state in odd-mass nuclei due to particle-vibration coupling provides a significant contribution to OES in charge radii.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

The role of magnetic fields in the stability and fragmentation of filamentary molecular clouds: two case studies at OMC-3 and OMC-4

We present the stability analysis of two regions, OMC-3 and OMC-4, in the massive and long molecular cloud complex of Orion A. We obtained 214 $\mu$m HAWC + /SOFIA polarization data, and we make use of archival data for the column density and C 18 O (1–0) emission line. We find clear depolarization in both observed regions and that the polarization fraction is anticorrelated with the column density and the polarization-angle dispersion function. We find that the filamentary cloud and dense clumps in OMC-3 are magnetically supercritical and strongly subvirial. This region should be in the gravitational collapse phase and is consistent with many young stellar objects (YSOs) forming in the region. Our histogram of relative orientation (HRO) analysis shows that the magnetic field is dynamically sub-dominant in the dense gas structures of OMC-3. We present the first polarization map of OMC-4. We find that the observed region is generally magnetically subcritical except for an elongated dense core, which could be a result of projection effect of a filamentary structure aligned close to the line of sight. The relative large velocity dispersion and the unusual positive shape parameters at high column densities in the HROs analysis suggest that our viewing angle may be close to axes of filamentary substructures in OMC-4. The dominating strong magnetic field in OMC-4 is unfavourable for star formation and is consistent with much fewer YSOs than in OMC-3.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Degradation and deforestation increase the sensitivity of the Amazon Forest to climate extremes

About 40% of the Brazilian Amazon has been deforested or suffered changes in forest structure through degradation (selective logging, fires, and fragmentation). The impact of forest degradation on the forest’s sensitivity to climate extremes has not been fully explored because of a lack of data and the complex interplay of forest structure and climate drivers. Here, we combined forest structure data from 545 airborne lidar transects (375 ha each) across the Brazilian Amazon with the Ecosystem Demography Model (ED2). We explore the forest’s functional response to near-present (1981–2019) climate extremes under observed forest structure from lidar ( Control ) and two forest structure change scenarios: (1) forest recovery by excluding all future deforestation and degradation ( Recovery ) and (2) expansion of selective logging and deforestation ( Degradation ). Using the Control simulation, we found a close and positive association between local forest aboveground biomass and the predicted gross primary productivity (GPP) and evapotranspiration (ET). Moreover, both GPP and ET respond negatively to extremes in vapor pressure deficit and downwelling shortwave irradiance in degraded forests in Eastern and Southern Amazon, indicating high sensitivity to droughts. Locally high-biomass forest patches showed little or no negative response of GPP and ET to extreme drought conditions whereas low-biomass forest patches in the same locations—typically degraded forest canopies—responded negatively to higher moisture stress. The results from the Recovery scenario showed similar results to simulations with observed structure; however, under the Degradation scenario, low-biomass forest patches became more abundant, resulting in more regions where GPP and ET are negatively impacted by hot drought conditions according to the ED2 model. Our results suggest that local forest structure is a critical determinant of an ecosystem’s response to climate variability, and that the loss of canopy trees in the Amazon through forest degradation could increase and expand forest vulnerability to droughts.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1

The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM (“SAR by X-ray Poses Quickly”) platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or “undruggable” targets, allows for (i) hit generation; (ii) the mapping of protein–ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.

59 BASIC BIOLOGICAL SCIENCES↗